Contacts of the helix formed by residues 123 - 146 (chain A) in PDB entry 3NC0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 3.4 20.3 - - + -
119A CYS 3.7 0.4 - - - -
120A VAL 3.0 26.0 - - - +
121A GLU* 2.5 20.1 + - - +
122A LYS* 1.3 81.0 - - - +
124A LYS* 1.3 61.3 + - - +
125A VAL* 2.6 37.2 + - + +
126A TYR 2.8 12.6 + - - -
127A ILE* 3.5 2.9 - - - +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A CYS* 3.8 20.8 + - - -
120A VAL* 3.9 28.6 + - + +
123A GLU* 1.3 75.1 + - - +
125A VAL* 1.3 52.2 + - + +
126A TYR 3.4 0.4 - - - -
127A ILE* 3.5 13.9 - - + +
128A GLY* 2.5 34.9 + - - -
165A GLN* 5.8 1.8 + - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 3.2 24.0 - - + -
77A TYR* 3.5 27.4 - - + -
123A GLU* 2.6 24.5 + - + +
124A LYS* 1.3 75.3 - - + +
126A TYR* 1.3 56.5 + - - +
128A GLY 3.8 0.3 - - - -
129A LYS* 2.9 29.8 + - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 3.4 14.4 - - + +
73A MET* 3.9 20.2 - - + -
76A LYS* 3.8 41.6 - - + +
77A TYR* 4.6 7.9 - - - -
80A LEU* 3.3 33.4 - - + -
109A LEU* 3.3 25.3 - - - +
112A LYS* 5.8 0.3 + - - -
113A THR* 3.8 19.7 - - + -
122A LYS* 4.3 13.0 - - + +
123A GLU 2.8 11.5 + - - +
125A VAL* 1.3 73.9 - - - +
127A ILE* 1.3 75.6 + - + +
129A LYS* 3.8 3.4 - - - +
130A LEU* 3.0 43.8 + - + +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 3.8 33.4 - - - +
114A SER* 4.1 12.8 - - - +
116A ASP* 5.9 0.4 - - + +
119A CYS* 3.9 22.9 - - + +
122A LYS* 3.6 17.0 - - + +
123A GLU 3.5 13.0 - - - +
124A LYS* 3.5 12.8 - - - +
126A TYR* 1.3 79.7 - - + +
128A GLY* 1.3 58.5 + - - +
130A LEU* 3.1 10.5 + - + +
131A ASN* 2.9 47.5 + - - +
166A ASN* 3.6 15.0 - - - +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS 2.5 22.3 + - - -
125A VAL* 3.8 1.1 - - - -
127A ILE* 1.3 73.6 - - - +
129A LYS* 1.3 56.9 + - - +
131A ASN* 3.5 11.3 + - - +
132A MET* 2.9 28.4 + - - +
169A VAL* 5.9 3.1 - - - -
173A LEU* 4.3 5.0 - - - +
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.3 41.7 + - + +
80A LEU* 4.1 18.8 - - + -
81A GLN* 4.7 12.8 - - - +
84A GLU* 3.3 41.8 + - - +
125A VAL 2.9 17.4 + - - +
126A TYR 3.8 4.0 - - - +
128A GLY* 1.3 72.3 - - - +
130A LEU* 1.3 61.8 + - - +
132A MET* 3.1 18.1 + - - +
133A ILE* 2.9 42.0 + - + +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.9 28.2 - - + +
83A LEU* 6.2 0.2 - - + -
106A VAL* 4.5 9.1 - - + +
109A LEU* 4.2 29.2 - - + +
110A ILE* 4.2 18.1 - - + +
113A THR* 3.3 26.0 - - - +
114A SER* 5.9 0.7 - - - +
126A TYR* 3.0 43.2 + - + +
127A ILE* 3.3 9.4 - - - +
129A LYS* 1.3 73.5 - - - +
131A ASN* 1.3 66.5 + - - +
133A ILE* 2.9 21.4 + - + +
134A LEU* 3.0 11.3 + - - +
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Residues in contact with ASN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.9 15.7 - - - +
114A SER* 4.9 0.4 - - - -
127A ILE* 2.9 33.2 + - - +
128A GLY* 3.6 9.4 - - - +
130A LEU* 1.3 71.6 - - - +
132A MET* 1.3 61.9 + - - +
134A LEU* 3.1 6.9 + - - +
135A VAL* 3.0 23.9 + - - +
166A ASN* 2.9 44.3 - - - +
169A VAL* 4.4 9.7 - - + +
170A ILE* 3.5 21.5 - - + +
173A LEU* 3.8 16.8 - - + -
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Residues in contact with MET 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 4.3 14.8 - - - +
128A GLY 2.9 15.5 + - - +
129A LYS* 3.2 22.4 - - - +
130A LEU 3.1 0.2 - - - -
131A ASN* 1.3 77.1 - - - +
133A ILE* 1.3 56.8 + - - +
135A VAL* 3.3 28.3 + - + -
136A GLN* 2.8 43.4 + - + +
139A LYS* 6.4 0.2 - - + -
173A LEU* 3.9 23.5 - - + +
177A GLU* 3.7 27.8 - - + +
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.5 54.5 - - + +
83A LEU* 4.3 8.1 - - + -
84A GLU* 4.3 12.3 - - + -
87A ILE* 3.4 27.6 - - + -
106A VAL* 4.2 19.1 - - + -
129A LYS* 2.9 25.8 + - + +
130A LEU* 2.9 12.1 + - + +
132A MET* 1.3 75.2 - - - +
134A LEU* 1.3 57.5 + - - +
136A GLN* 3.0 11.5 - - + +
137A ILE* 2.8 26.3 + - - +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 6.5 0.4 - - - -
106A VAL* 4.1 10.7 - - + +
107A VAL* 4.5 23.1 - - + -
110A ILE* 3.5 31.9 - - + -
130A LEU 3.0 5.7 + - - -
131A ASN 3.3 8.7 - - - +
133A ILE* 1.3 77.7 - - - +
135A VAL* 1.3 51.8 + - - +
137A ILE* 2.9 14.7 + - + +
138A LEU* 2.8 58.4 + - + +
146A TRP* 5.0 4.9 - - - +
149A PHE* 4.7 10.8 - - + -
153A ILE* 6.3 0.4 - - + -
170A ILE* 4.0 28.0 - - + -
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASN 3.0 15.6 + - - +
132A MET* 3.5 24.9 - - + +
134A LEU* 1.3 75.3 - - - +
136A GLN* 1.3 63.8 + - - +
138A LEU* 3.7 9.2 - - + +
139A LYS* 2.9 25.4 + - + +
170A ILE* 3.7 30.7 - - + +
173A LEU* 3.7 16.4 - - + -
174A LEU* 3.8 26.0 - - + +
177A GLU* 3.8 20.4 - - + -
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 3.1 30.0 + - + +
87A ILE* 3.9 13.8 - - + +
88A LYS* 3.1 46.6 - - + +
132A MET* 2.8 36.6 + - + +
133A ILE* 3.0 21.1 + - + +
135A VAL* 1.3 77.1 - - - +
137A ILE* 1.3 59.1 + - - +
139A LYS* 3.3 34.5 + - - +
140A GLN* 3.8 10.9 + - - +
177A GLU* 5.9 1.2 + - - -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 3.5 31.9 - - + -
91A TRP* 3.8 16.4 - - + -
102A ILE* 3.5 32.3 - - + -
103A LYS* 4.5 14.8 - - + -
106A VAL* 4.2 15.9 - - + -
133A ILE 2.8 9.6 + - - +
134A LEU* 2.9 17.0 + - + +
136A GLN* 1.3 73.0 - - - +
138A LEU* 1.3 57.6 + - - +
139A LYS 3.1 1.3 - - - -
140A GLN* 2.7 29.2 + - - +
141A GLU* 3.4 24.0 + - + +
146A TRP* 4.9 5.4 - - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 2.8 35.1 + - + +
135A VAL* 3.7 18.4 - - + +
137A ILE* 1.3 72.8 - - - +
139A LYS* 1.3 62.4 + - - +
140A GLN 2.8 0.2 + - - -
141A GLU* 3.0 0.4 + - - -
142A TRP* 2.7 45.0 + - + +
143A PRO* 4.5 1.4 - - - +
146A TRP* 4.1 17.0 - - + -
149A PHE* 3.4 60.3 - - + -
170A ILE* 4.7 3.1 - - + -
174A LEU* 4.1 23.8 - - + -
194A LEU* 4.8 2.2 - - - +
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Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 5.9 4.2 - - - +
132A MET* 6.4 0.2 - - + -
135A VAL* 2.9 14.1 + - + +
136A GLN* 3.3 32.1 + - - +
138A LEU* 1.3 75.9 - - - +
140A GLN* 1.3 54.8 + - + +
143A PRO* 6.0 0.2 - - - +
174A LEU* 5.1 3.7 - - + +
177A GLU* 3.1 44.7 + - + +
178A VAL* 5.5 4.9 - - + -
185A GLN* 3.8 19.2 + - - +
186A ILE* 3.7 36.5 - - + +
190A LYS* 2.7 36.5 + - - +
194A LEU* 4.2 17.2 - - + +
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE* 3.7 25.1 - - + +
88A LYS* 4.6 7.4 - - + +
91A TRP* 3.9 28.1 + - + +
92A LYS* 4.0 32.3 - - - +
136A GLN 3.9 10.5 - - - +
137A ILE* 2.7 19.5 + - - +
139A LYS* 1.3 73.9 - - + +
141A GLU* 1.3 59.8 + - - +
144A LYS* 5.6 0.9 - - - +
145A HIS* 5.3 0.9 - - - -
190A LYS* 4.0 18.7 + - - +
1024A GLU* 4.3 19.8 - - - +
1032A ASP* 4.9 8.1 - - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP* 3.6 27.0 + - - +
96A ARG* 4.2 7.1 + - - -
99A CYS* 4.8 3.5 - - - +
103A LYS* 3.0 42.2 + - - +
137A ILE* 3.8 13.4 - - + +
138A LEU 3.0 1.0 + - - -
139A LYS 3.6 0.4 - - - -
140A GLN* 1.3 82.3 - - - +
142A TRP* 1.3 73.9 + - - +
143A PRO* 2.8 10.5 - - - +
144A LYS* 3.1 8.7 + - - -
145A HIS* 3.1 51.1 + - + +
146A TRP* 3.7 8.6 + - + -
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Residues in contact with TRP 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 2.7 40.2 + - + +
141A GLU* 1.3 71.2 - - - +
143A PRO* 1.3 68.4 - - + +
146A TRP* 2.9 38.8 + - - +
147A PRO* 4.3 2.0 + - - +
149A PHE* 3.5 41.7 - + + +
150A ILE* 4.3 23.4 - - + +
174A LEU* 5.0 10.1 - - + -
178A VAL* 5.8 0.4 - - + -
194A LEU* 3.6 24.7 - - + -
197A SER* 3.1 52.7 - - - -
198A MET* 3.3 30.7 - - + -
201A GLU* 4.4 13.4 + - + -
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Residues in contact with PRO 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU 4.5 0.4 - - - +
139A LYS 6.0 0.2 - - - +
141A GLU* 3.2 4.7 - - - +
142A TRP* 1.3 112.9 - - + +
144A LYS* 1.3 78.8 + - + +
145A HIS 3.5 0.2 + - - -
147A PRO* 3.6 18.1 - - + +
193A HIS* 3.3 36.3 - - + +
194A LEU* 4.4 7.9 - - + -
197A SER* 3.9 16.4 - - - +
201A GLU* 6.0 1.6 - - - +
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLN 5.6 0.4 - - - +
141A GLU* 3.1 9.7 + - - +
143A PRO* 1.3 85.5 - - + +
145A HIS* 1.3 81.6 + - + +
146A TRP 3.9 0.2 + - - -
147A PRO* 4.1 8.7 - - - +
190A LYS* 6.4 1.8 - - - +
193A HIS* 3.2 37.6 + - + +
1032A ASP* 3.5 38.8 + - - +
1034A PHE* 4.4 13.8 - - - -
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.0 44.7 + - - +
103A LYS* 3.3 17.5 + - - -
140A GLN 5.3 0.7 - - - -
141A GLU* 3.1 33.8 + - + +
144A LYS* 1.3 93.5 + - + +
146A TRP* 1.3 58.7 + - - +
147A PRO* 3.3 9.3 - - - +
1030A THR* 5.9 1.2 - - - +
1032A ASP* 4.3 17.9 + - - -
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Residues in contact with TRP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 3.3 34.6 - - + +
107A VAL* 4.6 23.8 - - + +
134A LEU* 5.0 4.9 - - - +
137A ILE* 4.9 5.5 - - + +
138A LEU* 4.1 16.8 - - + +
141A GLU* 3.7 10.5 + - + +
142A TRP* 2.9 31.9 + - - +
145A HIS* 1.3 79.1 - - - +
147A PRO* 1.3 68.1 - - + +
148A THR* 3.4 17.0 - - - -
149A PHE* 3.1 60.2 + + + +
152A ASP* 3.5 14.4 - - + -
153A ILE* 6.2 0.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il